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Detailed information for vg0904255240:

Variant ID: vg0904255240 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 4255240
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTTTTATTCAAATTTTTTGTGCAAATATGAAAATATTTATGTCGTGCTTAAAGAACATTTTATGACAAATCAAGTCATAATAAAATAAATGATAATTA[C/T]
ATAAATTTTTTAAATAAGACAAATGGTCAAACGTTGGATAAAAAGTCAACGGCGTCATACATTAAAATATGGAGGTAGTATATATCTATCATTTTTATAA

Reverse complement sequence

TTATAAAAATGATAGATATATACTACCTCCATATTTTAATGTATGACGCCGTTGACTTTTTATCCAACGTTTGACCATTTGTCTTATTTAAAAAATTTAT[G/A]
TAATTATCATTTATTTTATTATGACTTGATTTGTCATAAAATGTTCTTTAAGCACGACATAAATATTTTCATATTTGCACAAAAAATTTGAATAAAACGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	5.50%	8.34%	27.61%	NA
All Indica	2759	43.00%	0.30%	13.16%	43.57%	NA
All Japonica	1512	83.50%	15.90%	0.13%	0.46%	NA
Aus	269	92.20%	0.00%	5.20%	2.60%	NA
Indica I	595	59.00%	1.00%	23.70%	16.30%	NA
Indica II	465	50.50%	0.00%	13.12%	36.34%	NA
Indica III	913	21.50%	0.00%	5.48%	73.06%	NA
Indica Intermediate	786	51.40%	0.30%	14.12%	34.22%	NA
Temperate Japonica	767	79.50%	20.30%	0.00%	0.13%	NA
Tropical Japonica	504	96.20%	2.80%	0.40%	0.60%	NA
Japonica Intermediate	241	69.70%	29.00%	0.00%	1.24%	NA
VI/Aromatic	96	14.60%	5.20%	6.25%	73.96%	NA
Intermediate	90	63.30%	6.70%	10.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0904255240	C -> DEL	N	N	silent_mutation	Average:31.66; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0904255240	C -> T	LOC_Os09g08190.1	downstream_gene_variant ; 3323.0bp to feature; MODIFIER	silent_mutation	Average:31.66; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0904255240	C -> T	LOC_Os09g08210.1	downstream_gene_variant ; 1837.0bp to feature; MODIFIER	silent_mutation	Average:31.66; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0904255240	C -> T	LOC_Os09g08190-LOC_Os09g08210	intergenic_region ; MODIFIER	silent_mutation	Average:31.66; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0904255240	NA	2.97E-06	mr1380_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0904255240	4.07E-06	NA	mr1546_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251